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Jamonnak N, Creamer TJ, Darby MM, Schaughency P, Wheelan SJ, Corden JL. Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing. RNA (NEW YORK, N.Y.) 2011; 17:2011-2025. [PMID: 21954178 PMCID: PMC3198594 DOI: 10.1261/rna.2840711] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 08/16/2011] [Indexed: 05/29/2023]
Abstract
RNA polymerase II transcribes both coding and noncoding genes, and termination of these different classes of transcripts is facilitated by different sets of termination factors. Pre-mRNAs are terminated through a process that is coupled to the cleavage/polyadenylation machinery, and noncoding RNAs in the yeast Saccharomyces cerevisiae are terminated through a pathway directed by the RNA-binding proteins Nrd1, Nab3, and the RNA helicase Sen1. We have used an in vivo cross-linking approach to map the binding sites of components of the yeast non-poly(A) termination pathway. We show here that Nrd1, Nab3, and Sen1 bind to a number of noncoding RNAs in an unexpected manner. Sen1 shows a preference for H/ACA over box C/D snoRNAs. Nrd1, which binds to snoRNA terminators, also binds to the upstream region of some snoRNA transcripts and to snoRNAs embedded in introns. We present results showing that several RNAs, including the telomerase RNA TLC1, require Nrd1 for proper processing. Binding of Nrd1 to transcripts from tRNA genes is another unexpected observation. We also observe RNA polymerase II binding to transcripts from RNA polymerase III genes, indicating a possible role for the Nrd1 pathway in surveillance of transcripts synthesized by the wrong polymerase. The binding targets of Nrd1 pathway components change in the absence of glucose, with Nrd1 and Nab3 showing a preference for binding to sites in the mature snoRNA and tRNAs. This suggests a novel role for Nrd1 and Nab3 in destruction of ncRNAs in response to nutrient limitation.
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Affiliation(s)
- Nuttara Jamonnak
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Tyler J. Creamer
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Miranda M. Darby
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Paul Schaughency
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Sarah J. Wheelan
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Jeffry L. Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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52
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Creamer TJ, Darby MM, Jamonnak N, Schaughency P, Hao H, Wheelan SJ, Corden JL. Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1. PLoS Genet 2011; 7:e1002329. [PMID: 22028667 PMCID: PMC3197677 DOI: 10.1371/journal.pgen.1002329] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 08/16/2011] [Indexed: 12/17/2022] Open
Abstract
RNA polymerase II synthesizes a diverse set of transcripts including both protein-coding and non-coding RNAs. One major difference between these two classes of transcripts is the mechanism of termination. Messenger RNA transcripts terminate downstream of the coding region in a process that is coupled to cleavage and polyadenylation reactions. Non-coding transcripts like Saccharomyces cerevisiae snoRNAs terminate in a process that requires the RNA–binding proteins Nrd1, Nab3, and Sen1. We report here the transcriptome-wide distribution of these termination factors. These data sets derived from in vivo protein–RNA cross-linking provide high-resolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3′ antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link efficiently to many expected non-coding RNAs but does cross-link to the 3′ end of most pre–mRNA transcripts, suggesting an extensive role in mRNA 3′ end formation and/or termination. Transcription in eukaryotes is widespread including both protein-coding transcripts and an increasing number of non-coding RNAs. Here we present the results of transcriptome-wide mapping of a set of yeast RNA–binding proteins that control expression of some protein-coding genes and a number of novel non-coding RNAs. The yeast Nrd1-Nab3-Sen1 pathway is required for termination and exosome-mediated processing of non-coding RNA polymerase II transcripts. Our data show that these components bind unexpected targets including a large number of antisense transcripts originating from the 3′ end of genes that are poorly expressed in the sense direction. We also show that Sen1 helicase, involved in termination of non-coding RNAs, is also present at the 3′ end of mRNAs, suggesting a more fundamental role in transcription termination. Mis-regulation of transcription is the underlying cause of many disease states. For example, mutation of the human Sen1 gene, senataxin, causes a range of neurodegenerative disorders. Understanding the roles of yeast RNA–binding proteins in controlling termination of coding and non-coding RNAs will be useful in deciphering the mechanism of these proteins in human cells.
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Affiliation(s)
- Tyler J. Creamer
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Miranda M. Darby
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nuttara Jamonnak
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Paul Schaughency
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Haiping Hao
- High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah J. Wheelan
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jeffry L. Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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53
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Unravelling the means to an end: RNA polymerase II transcription termination. Nat Rev Mol Cell Biol 2011; 12:283-94. [PMID: 21487437 DOI: 10.1038/nrm3098] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The pervasiveness of RNA synthesis in eukaryotes is largely the result of RNA polymerase II (Pol II)-mediated transcription, and termination of its activity is necessary to partition the genome and maintain the proper expression of neighbouring genes. Despite its ever-increasing biological significance, transcription termination remains one of the least understood processes in gene expression. However, recent mechanistic studies have revealed a striking convergence among several overlapping models of termination, including the poly(A)- and Sen1-dependent pathways, as well as new insights into the specificity of Pol II termination among its diverse gene targets. Broader knowledge of the role of Pol II carboxy-terminal domain phosphorylation in promoting alternative mechanisms of termination has also been gained.
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54
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Regulated antisense transcription controls expression of cell-type-specific genes in yeast. Mol Cell Biol 2011; 31:1701-9. [PMID: 21300780 DOI: 10.1128/mcb.01071-10] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptome profiling studies have recently uncovered a large number of noncoding RNA transcripts (ncRNAs) in eukaryotic organisms, and there is growing interest in their role in the cell. For example, in haploid Saccharomyces cerevisiae cells, the expression of an overlapping antisense ncRNA, referred to here as RME2 (Regulator of Meiosis 2), prevents IME4 expression. In diploid cells, the a1-α2 complex represses the transcription of RME2, allowing IME4 to be induced during meiosis. In this study we show that antisense transcription across the IME4 promoter region does not block transcription factors from binding and is not required for repression. Mutational analyses found that sequences within the IME4 open reading frame (ORF) are required for the repression mediated by RME2 transcription. These results support a model where transcription of RME2 blocks the elongation of the full-length IME4 transcript but not its initiation. We have found that another antisense transcript, called RME3, represses ZIP2 in a cell-type-specific manner. These results suggest that regulated antisense transcription may be a widespread mechanism for the control of gene expression and may account for the roles of some of the previously uncharacterized ncRNAs in yeast.
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55
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Harrison BR, Yazgan O, Krebs JE. Life without RNAi: noncoding RNAs and their functions in Saccharomyces cerevisiae. Biochem Cell Biol 2010; 87:767-79. [PMID: 19898526 DOI: 10.1139/o09-043] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There are a number of well-characterized and fundamental roles for noncoding RNAs (ncRNAs) in gene regulation in all kingdoms of life. ncRNAs, such as ribosomal RNAs, transfer RNAs, small nuclear RNAs, small nucleolar RNAs, and small interfering RNAs, can serve catalytic and scaffolding functions in transcription, messenger RNA processing, translation, and RNA degradation. Recently, our understanding of gene expression has been dramatically challenged by the identification of large and diverse populations of novel ncRNAs in the eukaryotic genomes surveyed thus far. Studies carried out using the budding yeast Saccharomyces cerevisiae indicate that at least some coding genes are regulated by these novel ncRNAs. S. cerevisiae lacks RNA interference (RNAi) and, thus, provides an ideal system for studying the RNAi-independent mechanisms of ncRNA-based gene regulation. The current picture of gene regulation is one of great unknowns, in which the transcriptional environment surrounding a given locus may have as much to do with its regulation as its DNA sequence or local chromatin structure. Drawing on the recent research in S. cerevisiae and other organisms, this review will discuss the identification of ncRNAs, their origins and processing, and several models that incorporate ncRNAs into the regulation of gene expression and chromatin structure.
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Affiliation(s)
- Benjamin R Harrison
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA
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56
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Koyama H, Ueda T, Ito T, Sekimizu K. Novel RNA polymerase II mutation suppresses transcriptional fidelity and oxidative stress sensitivity in rpb9Delta yeast. Genes Cells 2010; 15:151-9. [PMID: 20088966 DOI: 10.1111/j.1365-2443.2009.01372.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We previously reported that transcription elongation factor S-II and RNA polymerase II subunit Rpb9 maintain transcriptional fidelity and contribute to oxidative stress resistance in yeast. Here we examined whether other transcription elongation-related factors affect transcriptional fidelity in vivo. Among the 17 mutants of transcription elongation-related factors analyzed, most were not responsible for maintaining transcriptional fidelity. This finding indicates that transcriptional fidelity is controlled by a limited number of transcription elongation-related factors including S-II and Rpb9 and not by all transcription elongation-related factors. In contrast, by screening rpb9Delta cell revertants for sensitivity to the oxidant menadione, we identified a novel mutation in RNA polymerase II, rpb1-G730D, which suppressed both reduced transcriptional fidelity and oxidative stress sensitivity. These findings suggest that the maintenance of transcriptional fidelity that is mediated by transcription machinery directly confers oxidative stress resistance.
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Affiliation(s)
- Hiroshi Koyama
- Department of Microbiology, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
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57
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Jacquier A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 2009; 10:833-44. [PMID: 19920851 DOI: 10.1038/nrg2683] [Citation(s) in RCA: 318] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Over the past few years, techniques have been developed that have allowed the study of transcriptomes without bias from previous genome annotations, which has led to the discovery of a plethora of unexpected RNAs that have no obvious coding capacities. There are many different kinds of products that are generated by this pervasive transcription; this Review focuses on small non-coding RNAs (ncRNAs) that have been found to be associated with promoters in eukaryotes from animals to yeast. After comparing the different classes of such ncRNAs described in various studies, the Review discusses how the models proposed for their origins and their possible functions challenge previous views of the basic transcription process and its regulation.
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Affiliation(s)
- Alain Jacquier
- Unité de Génétique des Interactions Macromoléculaires, Institut Pasteur, Centre National de la Recherche Scientifique URA2171, 25 Rue du Dr Roux, F-75015, Paris, France.
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58
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59
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Richard P, Manley JL. Transcription termination by nuclear RNA polymerases. Genes Dev 2009; 23:1247-69. [PMID: 19487567 DOI: 10.1101/gad.1792809] [Citation(s) in RCA: 246] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Gene transcription in the cell nucleus is a complex and highly regulated process. Transcription in eukaryotes requires three distinct RNA polymerases, each of which employs its own mechanisms for initiation, elongation, and termination. Termination mechanisms vary considerably, ranging from relatively simple to exceptionally complex. In this review, we describe the present state of knowledge on how each of the three RNA polymerases terminates and how mechanisms are conserved, or vary, from yeast to human.
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Affiliation(s)
- Patricia Richard
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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60
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Belostotsky D. Exosome complex and pervasive transcription in eukaryotic genomes. Curr Opin Cell Biol 2009; 21:352-8. [DOI: 10.1016/j.ceb.2009.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 04/19/2009] [Accepted: 04/20/2009] [Indexed: 12/27/2022]
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61
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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62
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Corden JL. Yeast Pol II start-site selection: the long and the short of it. EMBO Rep 2008; 9:1084-6. [PMID: 18846104 DOI: 10.1038/embor.2008.192] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 09/18/2008] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.
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63
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Abstract
Recent work from Kuehner and Brow (2008) and Thiebaut et al. (2008) in Molecular Cell and Jenks et al. (2008) in Molecular and Cellular Biology reveals that regulated expression of central nucleotide synthesis pathway components directs start site-dependent RNA polymerase II termination.
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Affiliation(s)
- Bernhard Dichtl
- Institute of Molecular Biology, University of Zürich, CH-8057 Zürich, Switzerland.
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64
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Koyama H, Sumiya E, Nagata M, Ito T, Sekimizu K. Transcriptional repression of the IMD2 gene mediated by the transcriptional co-activator Sub1. Genes Cells 2008; 13:1113-26. [PMID: 18823333 DOI: 10.1111/j.1365-2443.2008.01229.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sub1 was originally identified as a transcriptional co-activator and later demonstrated to have pleiotropic functions during multiple transcription steps, including initiation, elongation and termination. The present study reveals a novel function of Sub1 as a transcription repressor in budding yeast. Sub1 does not activate IMP dehydrogenase 2 (IMD2) gene expression but rather represses its expression. First, we examined the genetic interaction of Sub1 with the transcription elongation factor S-II/TFIIS, which is encoded by the DST1 gene. Disruption of the SUB1 gene partially suppressed sensitivity to the transcription elongation inhibitor mycophenolate (MPA) in a dst1 gene deletion mutant. SUB1 gene deletion increased the expression level of the IMD2 gene, which confers resistance to MPA, indicating that Sub1 functions to repress IMD2 gene expression. Sub1 located around the promoter region of the IMD2 gene. The upstream region of the transcription start sites was required for Sub1 to repress the IMD2 gene expression. These results suggest that the transcriptional co-activator Sub1 also has a role in transcriptional repression during transcription initiation in vivo.
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Affiliation(s)
- Hiroshi Koyama
- Department of Microbiology, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
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65
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Kwapisz M, Wery M, Després D, Ghavi-Helm Y, Soutourina J, Thuriaux P, Lacroute F. Mutations of RNA polymerase II activate key genes of the nucleoside triphosphate biosynthetic pathways. EMBO J 2008; 27:2411-21. [PMID: 18716630 PMCID: PMC2525842 DOI: 10.1038/emboj.2008.165] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 07/30/2008] [Indexed: 01/22/2023] Open
Abstract
The yeast URA2 gene, encoding the rate-limiting enzyme of UTP biosynthesis, is transcriptionally activated by UTP shortage. In contrast to other genes of the UTP pathway, this activation is not governed by the Ppr1 activator. Moreover, it is not due to an increased recruitment of RNA polymerase II at the URA2 promoter, but to its much more effective progression beyond the URA2 mRNA start site(s). Regulatory mutants constitutively expressing URA2 resulted from cis-acting deletions upstream of the transcription initiator region, or from amino-acid replacements altering the RNA polymerase II Switch 1 loop domain, such as rpb1-L1397S. These two mutation classes allowed RNA polymerase to progress downstream of the URA2 mRNA start site(s). rpb1-L1397S had similar effects on IMD2 (IMP dehydrogenase) and URA8 (CTP synthase), and thus specifically activated the rate-limiting steps of UTP, GTP and CTP biosynthesis. These data suggest that the Switch 1 loop of RNA polymerase II, located at the downstream end of the transcription bubble, may operate as a specific sensor of the nucleoside triphosphates available for transcription.
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Affiliation(s)
- Marta Kwapisz
- CEA, iBiTec-S, Service de Biologie Intégrative et Génétique Moléculaire, Gif-sur-Yvette, France
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66
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Kuehner JN, Brow DA. Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. Mol Cell 2008; 31:201-11. [PMID: 18657503 DOI: 10.1016/j.molcel.2008.05.018] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 04/24/2008] [Accepted: 05/29/2008] [Indexed: 10/21/2022]
Abstract
Guanine nucleotide negatively regulates yeast inosine monophosphate dehydrogenase (IMPDH) mRNA synthesis by an unknown mechanism. IMPDH catalyzes the first dedicated step of GTP biosynthesis, and feedback control of its expression maintains the proper balance of purine nucleotides. Here we show that RNA polymerase II (Pol II) responds to GTP concentration. When GTP is sufficient, Pol II initiates transcription of the IMPDH gene (IMD2) at TATA box-proximal "G" sites, producing attenuated transcripts. When GTP is deficient, Pol II initiates at an "A" further downstream, circumventing the regulatory terminator to produce IMPDH mRNA. A major determinant for GTP concentration-dependent initiation at the upstream sites is the presence of guanine at the first and second positions of the transcript. Mutations in the Rpb1 subunit of Pol II and in TFIIB disrupt IMD2 regulation by altering start site selection. Thus, Pol II initiation can be regulated by the concentration of initiating nucleotide.
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Affiliation(s)
- Jason N Kuehner
- Cellular and Molecular Biology Graduate Program, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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